Ames, Ia. — Scientists at the National Animal Disease Center in Ames are eager to begin unraveling the mysteries of mad cow disease.

As part of their work, they will infect cattle with the altered protein that causes the fatal ailment that apparently can be transmitted to humans who consume infected beef. They will study the animals and dissect their carcasses after the livestock die.

But lab officials have found themselves besieged in the past few months by internal and public criticism for the way the facility handles body parts, blood, urine and feces of animals with other diseases caused by the same kind of altered protein responsible for mad cow.

So the lab has suspended the start of its study until federal, state and local officials can investigate its disposal practices and be assured that they don't endanger Iowans or the state's livestock industry.

Interviews with workers at the internationally prominent facility, along with a review of enforcement records, staff e-mails, meeting tapes and an analysis of nationwide industry standards, revealed a series of potentially devastating environmental and worker-safety flaws and defensiveness to scrutiny created by whistle-blowers.

The "NADC could be shut down" over reports of the problems, acting director Ronald Horst told workers at one point. Horst, who was the acting director of the lab for about 1years, returned to a research role in May.

The problems became public after two animal-care workers told their bosses and Ames city officials that they feared the lab wasn't properly treating diseased-animal wastes that eventually end up in the South Skunk River. The river doesn't provide city drinking water downstream from the lab, but it is used for fishing, canoeing and watering livestock.

Lab officials contend the heating system they use on the waste before it is sent to the Ames sewage plant and on to the river deactivates disease-causing agents. Ames city officials, knowing the city plant can't neutralize those substances, joined the lab in appointing a panel of international experts to review the lab's methods. In the meantime, the lab's procedures remain the same.

State health officials have downplayed the health risk to Iowans. Some animal diseases don't affect humans, and others would require a person to eat infected parts of an animal.

"I don't think anything here is a huge violation, but they are an indication that they need to look at management," Wayne Gieselman, who runs Iowa's environmental protection department, said of the lab's environmental issues. "People should be able to feel like they are safely running operations."

Since the sewage issue became public in May, the Des Moines Sunday Register has learned of several other instances in which the disease lab has run afoul of state and federal agencies for worker-safety and environmental lapses. The facility has racked up fines or proposed fines from the U.S. Environmental Protection Agency and the Iowa Department of Natural Resources, as well as citations from the U.S. Occupational Safety and Health Administration, which does not fine other federal agencies. The disease lab is a federal agency.

Animal waste as sewage

The sewage issue, however, seems to pose the greatest concern for Iowans and the livestock industry - and threatens the reputation of what is considered the nation's pre-eminent animal disease lab.

The 83-building center is located on the east side of Ames. The 304 employees - 62 of them scientists - study the most serious domestic poultry and livestock diseases. It's the animal-world equivalent of the Centers for Disease Control and Prevention in Atlanta, the leading federal research agency concerning human ailments.

Sandy Miller Hays, the spokeswoman for the Ames lab, defended the facility's practices. "NADC is run very well," she said. "We are proud of NADC. It is a star doing very important work."

Richard Auwerda and Timothy Gogerty are the two animal caretakers who went public with what they considered a serious problem: Their lab was using a less-elaborate safety system than its sister facility, the National Veterinary Services Laboratories, which is located on the same campus. Both agencies are part of the U.S. Department of Agriculture, but answer to different divisions of the USDA.

Auwerda and Gogerty assist scientists in performing necropsies - examinations of dead animals, some of which carry diseases that could devastate Iowa's livestock as well as elk and deer populations should they escape the research center.

For instance, in a necropsy the workers might cut the spine of an animal into pieces and split the brain in half with a meat saw. Those nervous-system tissues carry the prion - or altered protein - that causes diseases such as mad cow.

Comparing the labs

The room in Building 5 where workers perform necropsies has drains on the floor that eventually lead to the Ames sewage treatment plant and then into the South Skunk River. Workers flush tissue scraps, blood, urine and other items down the drain into a heated storage tank and then on to the city sewage plant.

The veterinary services lab on the same campus also has necropsy rooms with drains on the floor. At that facility, those drains are plugged during procedures, and workers haul out body parts and excretions to be incinerated. They use straw to soak up fluids and feces so that those substances can be burned, too.

Gogerty wondered why the disease lab wasn't following the same procedures as the veterinary services lab, - plugging the drain and using straw to soak up fluids - especially considering that they often work with animals with the same or similar diseases.

Auwerda had the same question.

"I think that is the safest way, because nothing is going down the drain," he said of the veterinary lab's procedures.

On Feb. 28, Auwerda received an unsolicited e-mail from Dr. Ronald Morgan, who is the head of animal resources at the veterinary services lab. His facility had been caring for elk infected with chronic wasting disease, and the remaining animals were going to be transferred to the disease lab. Morgan explained in the e-mail that the state veterinarian and biosafety and animal-welfare officials had demanded that his lab plug drains, provide bedding for the living animals and incinerate all wastes when working with chronic wasting disease.

"It is known that CWD is an environmental contaminant from work done at Colorado State University," Morgan wrote. "It most likely is a fecal contamination that occurs, but that is not entirely proven (a good research project). It is known the sewage treatment does not kill prions, and it is also known that CWD is coming this direction naturally."

Miller Hays said the disease lab uses a different - but still effective - method to deactivate prions because its heating and ventilation system can't handle the dust matter from straw that is needed to run a complete "bag and burn" disposal operation.

Auwerda said the disease lab used no bedding and left its drains open. It did incinerate most body parts, he said. Any leftover tissue fragments and fluids that go down the drain are heated at 250 degrees for 30 minutes in a storage tank, lab officials said.

They say the heat is enough to deactivate the prions, but that is still a matter of scientific debate.

Auwerda said the disease lab's own manual seems to require that the wastes be held in bleach for a half-hour or more before the heating, to be doubly sure the prions are deactivated. That's not what happens in practice, he said.

Miller Hays said she didn't know whether the disease lab would change its procedures after it moves to a new half-billion-dollar facility next year.

Meanwhile, the review panel will meet through the summer to study the disease lab's sewage treatment practices, and the mad cow experiments that were to start on May 11 remain on hold. All other work - and waste-disposal procedures - continue as before.